Week 14 (11/28 – 12/2)
Inhibition Assays - on 2 compounds
Tues Nov. 29th - FINAL PRESENTATIONS of Enzyme Inhibition Graphs- everyone
make a one slide PowerPoint and upload to the GroupMeetingSlides/FInalSlides_StudentsFall11 folder on GDocs
save file with your name and date in the file name
Thurs (12/1) - Lab Cleanup (Required) - each students spends 1 hr cleaning in lab (counts as 1 hour of lab time) Fri (12/2) - Lab Cleanup (Required) - each students spends 1 hr cleaning in lab (counts as 1 hour of lab time)
Sat ( 12/3) Final Report due (5:00 pm ) Final Lab Notebook check (7:00 pm)
Final Wikispaces check
1st Week (8/31 – 9/2) PAPER COPY – Print out of TxClass Safety Training (can put in Safety section of VDS sign-in binder in lab)
Pick target from current list
TUES: (after class)
Create a GDocs folder
Create a Wikispaces page
Analyze DNA sequence exercise (in WELCH computer lab) - save result to your GDocs folder
WED - FRI:
- download protocols from GDocs under /Protocols/Cloning/FirstProtocols
Submit to DNA Sequencing - save results to your GDocs folder
RE Digest - save results to your GDocs folder and post image and commentary to your Wikispace page
PCR - of pGBR22 - save results to your GDocs folder and post image and commentary to your Wikispace page
2nd Week (9/5 – 9/9)
Print out of TxClass Safety Training -
PAPER COPY – put in Safety section of VDS sign-in binder in lab
Check on line (DNA Sequencing core website) for your results from "Submit to DNA Sequencing" - save results to your GDocs folder
Finish up PCR - this PCR must work correctly before you can proceed - Post final, properly labeled image to your Wikispaces page (Research Pages section) and, of course, in your labnoteook
Finish up RE Digest - Post final, properly labeled image to your Wikispaces page and labnoteook
Once you have chosen your target: Protocol Primer Design for Overlap PCR - post final primers to Wikispaces page
ProtocolPCR_PrimerDesign_for_pNIC-Bsa4Cloning.doc
Wikispaces check on each Friday
Your WikiPage should have
images of all PCR gels (well annotated - i.e. descriptions and what each lane is)
image of RE digest gel (well annotated)
Paste a copy of your DNA sequence from the DNA sequencing core (briefly describe what it is)
3rd Week (9/12 – 9/16)
PyMol Refresher (see Announcement page for PyMol Help Session on Thursday 9/14)
Due next week for Returning Spring VDSers
Due week after next for New VDSers (Joshua, Hong, Marshall, Shreya, Indra)
Primary PCR with Oligo Mix ProtocolPCR_PrimerOverlapVDS_Fall11.docx
Secondary PCR w/ Tail primers same protocol
For Virtual Refresher:
Since the blades are full - you only need to have your first Run started by the end of this week. (by Friday 9/30)
VDSers that are returning from Spring:
Begin realVirtual Screening - prepare protein in GOLD and start jobs (cb306 should be done this week and the next one started)
Wikispaces check on each Friday Week 6 (10/3 – 10/7) Submit 2nd job of Virtual Screen Refresher Begin Virtual Screening on YOUR targetVirtual Screening
Continue cloning
complete both primer design exercises
complete 1st and 2nd Overlap PCR
Lab Notebook check this Friday (7:00 pm)
Wikispaces check on each Friday
Target Selection exercise ?
10/03/11 - Still need PyMol Refresher from: Michael E., Shutian J., Giancarlo M., Shreya N., Indra S. , Hong C.
Week 7 (10/10 – 10/14)
Journal Club 3
Research Report Due - Tues Oct. 11th - Guidelines in GDocs folder
Continue realVirtual Screening - prepare protein in GOLD and start jobs
Virtual Screening help session for setting up your protein (should have 1st library done this week)
Week 9 (10/24 – 10/28) VIRTUAL SCREENING - finish by this week - do Top Ligands Procotol to get final compounds for ordering
Journal Club 4
Express your enzyme Fri ( 10/28) Lab Notebook check this Friday(7:00 pm)
or Sat night if working on Sat.
Wikispaces check on each Friday
Week 10 (10/31 – 11/4) Tues Nov. 1st Thursday Nov 3rd at Midnight (Materials & Methods for Cloning due) FRI External Open House - Wednesday Nov. 2nd 1- 4 pm
Top Ligands Procotol to get final compounds for ordering
Express your enzyme
Purify and Characterize your protein
Wikispaces check on each Friday
Protein Expression Scheduling:
Here's the Sign Up Form on Google - new guys and returning Spring VDSers should fill this out by Monday night.
Week 11 (11/7 – 11/11)
Journal Club 5
Tues Nov. 8th at Midnight (Materials & Methods for Virtual Screening due) - see Tips & Hints page
Enzyme Assays
Wikispaces check on each Friday Week 12 (11/14 – 11/18) Tues Nov. 15th at Midnight (Materials & Methods for Expression, Purification, and Characterization due)
Purify and Characterize your protein - NOTE: this is a long and arduous process. Don't put it off.
Enzyme Assays
Inhibition Assays Fri ( 11/18) Lab Notebook check this Friday(7:00 pm)
or Sat night if working on Sat.
Wikispaces check on each Friday
Protein Protocols to be completed - also see instructional videos on GDocs
ProtocolProteinExpression_VDS_Fall11_ver2.doc
ProtocolProteinPurificationVDS_Fall11.doc ProtocolHomemadeSDSPageGelSolutionsVDS_Fall11.docx - Skip this one (the Mentors will make gels for you)
ProtocolProteinCharacterizationVDS_Fall11.doc
ProtocolFPLC_GelFiltration_VDS_Fall11V_v2.docx
ProtocolLabEnzymeTest_Phosphatase_VDS_Fall11.xlsx
Then on to Inhibition Assays once compounds arrive
Week 13 (11/21 – 11/25): Thanksgiving
Journal Club 6
Inhibition Assays - on 2 compounds
Wikispaces check on each Friday
Week 14 (11/28 – 12/2)
Inhibition Assays - on 2 compounds
Tues Nov. 29th - FINAL PRESENTATIONS of Enzyme Inhibition Graphs- everyone
make a one slide PowerPoint and upload to the GroupMeetingSlides/FInalSlides_StudentsFall11 folder on GDocs
save file with your name and date in the file name
Thurs (12/1) - Lab Cleanup (Required) - each students spends 1 hr cleaning in lab (counts as 1 hour of lab time)
Fri (12/2) - Lab Cleanup (Required) - each students spends 1 hr cleaning in lab (counts as 1 hour of lab time)
Sat ( 12/3)
Final Report due (5:00 pm )
Final Lab Notebook check (7:00 pm)
Final Wikispaces check
1st Week (8/31 – 9/2)
PAPER COPY – Print out of TxClass Safety Training (can put in Safety section of VDS sign-in binder in lab)
Pick target from current list
TUES: (after class)
Create a GDocs folder
Create a Wikispaces page
Analyze DNA sequence exercise (in WELCH computer lab) - save result to your GDocs folder
WED - FRI:
- download protocols from GDocs under /Protocols/Cloning/FirstProtocols
Submit to DNA Sequencing - save results to your GDocs folder
RE Digest - save results to your GDocs folder and post image and commentary to your Wikispace page
PCR - of pGBR22 - save results to your GDocs folder and post image and commentary to your Wikispace page
2nd Week (9/5 – 9/9)
Your WikiPage should have
3rd Week (9/12 – 9/16)
PyMol Refresher (see Announcement page for PyMol Help Session on Thursday 9/14)
Once you have successfully completed first PCR,
Science Works assignment due Friday Sept 16th - see announcement page
Lab Notebook Check this Friday - leave your notebook in 'Drug Screening Notebooks' drawer in lab by 7:00 pm
- all protocols (PCR , RE Digest, analyze DNA, submit DNA)
- all gel images
- Analyze DNA Sequence exercise work
- Protocol, Order form and Results from ProtocolDNASequencingFacilityVDS_Fall11.doc
Wikispaces check on each Friday4th Week (9/19 – 9/23)
PyMol Refresher
Virtual Screen Refresher - due next week (Tues 9/27)
Wikispaces check on each Friday
Week 5 (9/26 – 9/30)
begin cloning
For Virtual Refresher:
Since the blades are full - you only need to have your first Run started by the end of this week. (by Friday 9/30)
VDSers that are returning from Spring:
Wikispaces check on each Friday
Week 6 (10/3 – 10/7)
Submit 2nd job of Virtual Screen Refresher
Begin Virtual Screening on YOUR target Virtual Screening
Continue cloning
Lab Notebook check this Friday (7:00 pm)
Wikispaces check on each Friday
Target Selection exercise ?
10/03/11 - Still need PyMol Refresher from: Michael E., Shutian J., Giancarlo M., Shreya N., Indra S. , Hong C.
Week 7 (10/10 – 10/14)
Journal Club 3
Research Report Due - Tues Oct. 11th - Guidelines in GDocs folder
Continue real Virtual Screening - prepare protein in GOLD and start jobs
PyMol Image contest Due Friday at Midnight
Wikispaces check on each Friday
Week 8 (10/17 – 10/21)
VIRTUAL SCREENING - should have 3 libraries completed.
Perform cloning protocol on your target:
- ProtocolpNIC-Bsa4_cloningVDS_Fall11.doc
verify positive clones with- ProtocolDNASequencingFacilitypNIC-Bsa4_VDS_Fall11.doc
Wikispaces check on each FridayWeek 9 (10/24 – 10/28)
VIRTUAL SCREENING - finish by this week - do Top Ligands Procotol to get final compounds for ordering
Journal Club 4
Express your enzyme
Fri ( 10/28) Lab Notebook check this Friday(7:00 pm)
or Sat night if working on Sat.
Wikispaces check on each Friday
Week 10 (10/31 – 11/4)
Tues Nov. 1st Thursday Nov 3rd at Midnight (Materials & Methods for Cloning due)
FRI External Open House - Wednesday Nov. 2nd 1- 4 pm
Top Ligands Procotol to get final compounds for ordering
Express your enzyme
Purify and Characterize your protein
Wikispaces check on each Friday
Protein Expression Scheduling:
Here's the Sign Up Form on Google - new guys and returning Spring VDSers should fill this out by Monday night.Week 11 (11/7 – 11/11)
Journal Club 5
Tues Nov. 8th at Midnight (Materials & Methods for Virtual Screening due) - see Tips & Hints page
Enzyme Assays
Wikispaces check on each Friday
Week 12 (11/14 – 11/18)
Tues Nov. 15th at Midnight (Materials & Methods for Expression, Purification, and Characterization due)
Purify and Characterize your protein - NOTE: this is a long and arduous process. Don't put it off.
Enzyme Assays
Inhibition Assays
Fri ( 11/18) Lab Notebook check this Friday(7:00 pm)
or Sat night if working on Sat.
Wikispaces check on each Friday
Protein Protocols to be completed - also see instructional videos on GDocs
ProtocolProteinExpression_VDS_Fall11_ver2.docProtocolProteinPurificationVDS_Fall11.doc
ProtocolHomemadeSDSPageGelSolutionsVDS_Fall11.docx - Skip this one (the Mentors will make gels for you)
ProtocolProteinCharacterizationVDS_Fall11.doc
ProtocolFPLC_GelFiltration_VDS_Fall11V_v2.docx
ProtocolLabEnzymeTest_Phosphatase_VDS_Fall11.xlsx
Then on to Inhibition Assays once compounds arrive
Week 13 (11/21 – 11/25): Thanksgiving
Journal Club 6
Inhibition Assays - on 2 compounds
Wikispaces check on each Friday